6DUX

2.25 Angstrom Resolution Crystal Structure of 6-phospho-alpha-glucosidase from Klebsiella pneumoniae in Complex with NAD.


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7292Protein: 10.3 mg/ml, 0.01M Tris-HCl pH 8.3, 2mM NAD; Screen: Classics II (B11) 2.1M DL-malic acid pH 7.0; Cryo: Screen + 20% glycerol.
Crystal Properties
Matthews coefficientSolvent content
2.4148.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 85.226α = 90
b = 85.226β = 90
c = 228.858γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDC(111)2018-06-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-F0.97872APS21-ID-F

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym I (Observed)Rrim I (All)Rpim I (All)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.25301000.1020.1020.1090.03722.98.546596-340.2
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.252.291000.7820.7820.8320.2820.85438.6

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONSADTHROUGHOUT2.2529.8944168235899.810.156120.154270.19129RANDOM49.003
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
0.940.470.94-3.05
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.14
r_dihedral_angle_4_deg13.259
r_dihedral_angle_3_deg10.27
r_long_range_B_refined5.737
r_long_range_B_other5.628
r_scangle_other3.599
r_dihedral_angle_1_deg3.272
r_mcangle_it2.65
r_mcangle_other2.649
r_scbond_it2.34
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.14
r_dihedral_angle_4_deg13.259
r_dihedral_angle_3_deg10.27
r_long_range_B_refined5.737
r_long_range_B_other5.628
r_scangle_other3.599
r_dihedral_angle_1_deg3.272
r_mcangle_it2.65
r_mcangle_other2.649
r_scbond_it2.34
r_scbond_other2.339
r_mcbond_it1.709
r_mcbond_other1.705
r_angle_refined_deg1.365
r_angle_other_deg0.444
r_chiral_restr0.068
r_gen_planes_refined0.041
r_gen_planes_other0.037
r_bond_refined_d0.007
r_bond_other_d0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6807
Nucleic Acid Atoms
Solvent Atoms359
Heterogen Atoms122

Software

Software
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing